Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.4+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0 |
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0 |
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.5 |
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.3.3 |
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.3.2 |
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.3.1 |
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.19.3.0 |
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.18.0.0 |
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.12.5.0 |
toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.12.4.0 |
fastp |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
fastp | 0.23.4 | package |
Additional information about this tool |
#import re ## Link input files #set ext = '.fastq' #if $single_paired.single_paired_selector == 'paired_collection': #if $single_paired.paired_input.forward.is_of_type('fastq.gz'): #set ext = '.fastq.gz' #end if #set $in1 = $single_paired.paired_input.forward #set $in2 = $single_paired.paired_input.reverse #set $in1_name = re.sub('[^\w\-\s]', '_', str($single_paired.paired_input.name)) + $ext #set $in2_name = re.sub('[^\w\-\s]', '_', str("%s_%s" % ($single_paired.paired_input.name, "R2"))) + $ext #set out1 = $output_paired_coll.forward #set out2 = $output_paired_coll.reverse ln -sf '$in1' '$in1_name' && ln -sf '$in2' '$in2_name' && #else #if $in1.is_of_type('fastq.gz') #set ext = '.fastq.gz' #end if #set $in1_name = re.sub('[^\w\-\s]', '_', str($in1.element_identifier)) + $ext ln -sf '$in1' '$in1_name' && #if str($single_paired.single_paired_selector) == 'paired': #set $in2_name = re.sub('[^\w\-\s]', '_', str("%s_R2" % $in2.element_identifier)) + $ext ln -sf '$in2' '$in2_name' && #end if #end if ## Run fastp fastp --thread \${GALAXY_SLOTS:-1} --report_title 'fastp report for $in1_name' #if $in1.is_of_type('fastqillumina', 'fastqsolexa', 'fastqillumina.gz', 'fastqsolexa.gz'): --phred64 #end if -i '$in1_name' -o first${ext} #if str($single_paired.single_paired_selector).startswith('paired'): -I '$in2_name' -O second${ext} #end if ## Adapter Trimming Options $single_paired.adapter_trimming_options.disable_adapter_trimming #if str($single_paired.adapter_trimming_options.adapter_sequence1): --adapter_sequence '$single_paired.adapter_trimming_options.adapter_sequence1' #end if #if str($single_paired.single_paired_selector).startswith('paired'): #if str($single_paired.adapter_trimming_options.adapter_sequence2): --adapter_sequence_r2 '$single_paired.adapter_trimming_options.adapter_sequence2' #else --detect_adapter_for_pe #end if #end if ## Global Trimming Options #if str($single_paired.global_trimming_options.trim_front1): -f $single_paired.global_trimming_options.trim_front1 #end if #if str($single_paired.global_trimming_options.trim_tail1): -t $single_paired.global_trimming_options.trim_tail1 #end if #if str($single_paired.single_paired_selector).startswith('paired'): #if str($single_paired.global_trimming_options.trim_front2): -F $single_paired.global_trimming_options.trim_front2 #end if #if str($single_paired.global_trimming_options.trim_tail2): -T $single_paired.global_trimming_options.trim_tail2 #end if #end if ## Overrepresented sequence analysis $overrepresented_sequence_analysis.overrepresentation_analysis #if str($overrepresented_sequence_analysis.overrepresentation_sampling): -P $overrepresented_sequence_analysis.overrepresentation_sampling #end if ## Filter Options ## Quality filtering options $filter_options.quality_filtering_options.disable_quality_filtering #if str($filter_options.quality_filtering_options.qualified_quality_phred): -q $filter_options.quality_filtering_options.qualified_quality_phred #end if #if str($filter_options.quality_filtering_options.unqualified_percent_limit): -u $filter_options.quality_filtering_options.unqualified_percent_limit #end if #if str($filter_options.quality_filtering_options.n_base_limit): -n $filter_options.quality_filtering_options.n_base_limit #end if ## Length filtering options $filter_options.length_filtering_options.disable_length_filtering #if str($filter_options.length_filtering_options.length_required): -l $filter_options.length_filtering_options.length_required #end if #if str($filter_options.length_filtering_options.length_limit): --length_limit $filter_options.length_filtering_options.length_limit #end if ## Low complexity filtering options $filter_options.low_complexity_filter.enable_low_complexity_filter #if str($filter_options.low_complexity_filter.complexity_threshold): -Y $filter_options.low_complexity_filter.complexity_threshold #end if ## Read Modification Options ## PolyG tail trimming, useful for NextSeq/NovaSeq data #if $read_mod_options.polyg_tail_trimming.trimming_select in ['', '-g']: #if str($read_mod_options.polyg_tail_trimming.poly_g_min_len): --poly_g_min_len $read_mod_options.polyg_tail_trimming.poly_g_min_len #end if $read_mod_options.polyg_tail_trimming.trimming_select #end if ## PolyX tail trimming #if $read_mod_options.polyx_tail_trimming.polyx_trimming_select == '-x': $read_mod_options.polyx_tail_trimming.polyx_trimming_select #if str($read_mod_options.polyx_tail_trimming.poly_x_min_len): --poly_x_min_len $read_mod_options.polyx_tail_trimming.poly_x_min_len #end if #end if ## UMI processing #if $read_mod_options.umi_processing.umi: $read_mod_options.umi_processing.umi #if str($read_mod_options.umi_processing.umi_loc): --umi_loc '$read_mod_options.umi_processing.umi_loc' #end if #if str($read_mod_options.umi_processing.umi_len): --umi_len $read_mod_options.umi_processing.umi_len #end if #if str($read_mod_options.umi_processing.umi_prefix): --umi_prefix '$read_mod_options.umi_processing.umi_prefix' #end if #end if ## Per read cutting by quality options #if $read_mod_options.cutting_by_quality_options.cut_by_quality5 or $read_mod_options.cutting_by_quality_options.cut_by_quality3: $read_mod_options.cutting_by_quality_options.cut_by_quality5 $read_mod_options.cutting_by_quality_options.cut_by_quality3 #if str($read_mod_options.cutting_by_quality_options.cut_window_size): -W $read_mod_options.cutting_by_quality_options.cut_window_size #end if #if str($read_mod_options.cutting_by_quality_options.cut_mean_quality): -M $read_mod_options.cutting_by_quality_options.cut_mean_quality #end if #end if ## Base correction by overlap analysis options $read_mod_options.base_correction_options.correction && mv first${ext} '${out1}' #if str($single_paired.single_paired_selector).startswith('paired'): && mv second${ext} '${out2}' #end if
Functional tests |
name | inputs | outputs | required files |
Test-1 |
single_paired|in1: R1.fq single_paired|single_paired_selector: single |
name: value name: value |
R1.fq value |
Test-2 |
single_paired|paired_input: paired collection single_paired|single_paired_selector: paired_collection |
name: value |
bwa-mem-fastq1.fq bwa-mem-fastq2.fq value |
Test-3 |
single_paired|in1: R1.fq single_paired|adapter_trimming_options|adapter_sequence1: ATCG single_paired|single_paired_selector: single |
name: value |
R1.fq value |
Test-4 |
single_paired|in1: R1.fq single_paired|single_paired_selector: single read_mod_options|umi_processing|umi: True read_mod_options|umi_processing|umi_loc: read1 read_mod_options|umi_processing|umi_len: 8 |
name: value |
R1.fq value |
Test-5 |
single_paired|in1: R1.fq single_paired|single_paired_selector: single read_mod_options|umi_processing|umi: True read_mod_options|umi_processing|umi_loc: read1 read_mod_options|umi_processing|umi_len: 12 |
name: value |
R1.fq value |
Test-6 |
single_paired|in1: bwa-mem-fastq1.fq single_paired|in2: bwa-mem-fastq2.fq single_paired|single_paired_selector: paired |
name: value name: value |
bwa-mem-fastq1.fq bwa-mem-fastq2.fq value |
Test-7 |
single_paired|in1: bwa-mem-fastq1.fq single_paired|in2: bwa-mem-fastq2.fq single_paired|single_paired_selector: paired read_mod_options|umi_processing|umi: True read_mod_options|umi_processing|umi_loc: read1 read_mod_options|umi_processing|umi_len: 8 |
name: value name: value |
bwa-mem-fastq1.fq bwa-mem-fastq2.fq value |
Test-8 |
single_paired|in1: bwa-mem-fastq1.fq single_paired|in2: bwa-mem-fastq2.fq single_paired|single_paired_selector: paired read_mod_options|umi_processing|umi: True read_mod_options|umi_processing|umi_loc: read2 read_mod_options|umi_processing|umi_len: 8 |
name: value name: value |
bwa-mem-fastq1.fq bwa-mem-fastq2.fq value |
Test-9 |
single_paired|in1: R1.fq single_paired|single_paired_selector: single output_options|report_html: False output_options|report_json: True |
name: value name: value |
R1.fq value |
Test-10 |
single_paired|in1: R1.fq.gz single_paired|single_paired_selector: single read_mod_options|polyg_tail_trimming|poly_g_min_len: 10 read_mod_options|polyg_tail_trimming|trimming_select: -g |
name: value |
R1.fq.gz value |
Test-11 |
single_paired|in1: R1.fq.gz single_paired|single_paired_selector: single read_mod_options|polyg_tail_trimming|trimming_select: -G read_mod_options|polyx_tail_trimming|poly_x_min_len: 10 read_mod_options|polyx_tail_trimming|polyx_trimming_select: -x |
name: value |
R1.fq.gz value |
Test-12 |
single_paired|paired_input: paired collection single_paired|single_paired_selector: paired_collection |
bwa-mem-fastq1.fq bwa-mem-fastq2_too_long.fq |